Maize Genomics and Genetics 2025, Vol.16, No.6, 284-293 http://cropscipublisher.com/index.php/mgg 290 Research that links metabolite biomarkers to genetic mapping studies has identified three essential genes which control stress-responsive metabolic traits through their production of citrate synthase and glucosyltransferase and cytochrome P450 (Liang et al., 2021; Zhao et al., 2023). The research confirms biomarkers function as predictive indicators while revealing specific molecular targets which scientists can use for marker-assisted selection and genomic breeding of salt-resistant maize. 6 Breeding and Translational Applications 6.1 Metabolite-QTL mapping and metabolome-wide association studies link metabolites with genetic loci The combination of metabolomics with quantitative genetics enables scientists to study how genetics affects salt tolerance in maize through advanced methods. The identification of metabolite quantitative trait loci (mQTLs) reveals genetic regions that control how metabolite levels respond to plant stress conditions. The genetic regions that control proline and sugar and secondary metabolite levels under stress conditions also contain QTLs that affect ion balance and biomass production (Liang et al., 2021; Brar et al., 2025). Scientists use natural diversity analysis with mGWAS to study how specific genetic variations called SNPs affect metabolite variations which helps them identify exact genetic influences on physical traits. The mGWAS research has identified three genes which encode citrate synthase and glucosyltransferases and cytochrome P450s that show strong links to both metabolite levels and salt tolerance under osmotic stress (Liang et al., 2021; Brar et al., 2025). The research methods allow scientists to connect genetic data with metabolic features which results in the identification of precise targets for developing salt-resistant maize varieties. 6.2 Functional validation of candidate genes strengthens causal links The identification of key genomic regions through QTL mapping and association studies requires functional validation to demonstrate their causal effects. The candidate genes that mQTL or mGWAS identify can be tested using reverse genetics methods and CRISPR-Cas9 genome editing and transgenic overexpression techniques. The study by Liang et al. (2021) shows that P5CS gene overexpression produces more proline which enhances salt tolerance but changes in raffinose biosynthesis and flavonoid pathways create new metabolites that boost salt tolerance in maize. (Brar et al., 2025). The process of functional validation proves the metabolic function of specific genes while showing how transcription factors and enzymes and metabolites interact with each other in a hierarchical manner. The research process leads to the identification of specific molecular targets which scientists can use for developing salt-resistant maize through breeding and genetic engineering. 6.3 Metabolomics-driven strategies accelerate molecular breeding and precision agriculture Metabolomics shows its potential for translation because it enables researchers to develop sophisticated breeding methods which improve agricultural practices for crop cultivation. The use of metabolite biomarkers in breeding programs enables fast germplasm population selection through marker-assisted and genomic selection methods. The research by Liang et al. (2021) shows that using metabolomic data with genomic prediction models results in enhanced salt tolerance predictions for untested genotypes. (Brar et al., 2025). Molecular design breeding requires basic knowledge of metabolic pathways to introduce specific alleles that control metabolite production through targeted editing or introgression techniques. Metabolomics helps precision agriculture through stress onset signature detection which enables early warning systems for prompt action. Scientists monitor maize under salinity stress through real-time field assessments by tracking metabolic markers in leaf tissues and root exudates using non-invasive methods. The application of metabolomics-based methods accelerates salt-resistant maize variety development which supports environmentally friendly farming practices and food security needs in areas where salt levels continue to rise (Liang et al., 2021; Brar et al., 2025). 7 Case Studies in Metabolomics of Maize Salt Stress 7.1 Metabolomic profiling of salt-tolerant maize revealed the central role of osmoprotectants The metabolic analysis of salt-tolerant maize reveals that proline and raffinose function as vital protective compounds which safeguard the plant. The LC-MS analysis of tolerant and sensitive inbred lines under saline conditions showed tolerant genotypes accumulated more proline and raffinose but sensitive lines did not show
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